We evaluated a combination of two temperatures and two packaging materials for long-term storage of vacuum-packaged (VP) beef striploins. Microbial populations and microbiome composition were monitored during refrigerated storage (120 days between 0–1.5 °C) and refrigerated-then-frozen storage (28 days between 0–1.5 °C then 92 days at −20 °C) under low-O2 permeability VP and high-O2 permeability VP with an antimicrobial (VPAM). Pseudomonas (PSE) and Enterobacteriaceae (EB) counts in VPAM samples were significantly higher (p < 0.05) than in VP samples at 28, 45, 90, and 120 days of storage. Microbiome data showed that bacteria of the genera Serratia and Brochothrix were more abundant in VPAM samples at 120 days, while lactic acid bacteria (LAB) dominated in VP samples. Frozen temperatures inhibited microbial growth and maintained a relatively stable microbiome. Refrigerated and frozen VPAM samples showed the greatest difference in the predicted metabolic functions at the end of storage driven by the microbiome composition, dominated by PSE and LAB, respectively. Although no signs of visible meat deterioration were observed in any sample, this study suggests that VP meat refrigerated and then frozen achieved better microbiological indicators at the end of the storage period.